Syllabus

Extended Syllabus PDF

Book

The Book of R - PDF

Last Week

Course Home Page LINK

Week 1 - Presentation LINK

What is Unix?

• UNIX is a computer operating system.
• It was first developed in 1969 at Bell Labs.
• In 1972, the Unix code was rewritten with the new C programming language.

(Dennis, Ken)

What is GNU?

• A wildebeest (or gnu) is an animal. Lives in Africa.
• GNU is the name of a computer operating system.
• The GNU project was started by Richard Stallman in 1983.
• GNU’s Not Unix!
• Fully free to modify, share and publish.

What is Linux (or GNU/Linux) ?

• Linux (or GNU/Linux) is a Unix-like operating system.
• GNU did not have all the parts.
• The kernel (GNU Hurd) is not yet completely built.
• In 1991 Linus Torvalds began to work -> Linux kernel.

How is Unix different from Linux?

• Linux does not use code from UNIX.

• The idea and names of commands are similar.

GNU/Linux Distributions

Linux_Distribution_Timeline

Terminal

A computer terminal is a hardware device that is used for entering data into, and displaying or printing data from a computer or a computing system.

Terminal

Basic GNU/Linux Commands

• Frequently Used Terms

• Directory Commands

• File Commands

• Special Commands

• vi Editor, Print Commands and Symbols

Frequently Used Terms

• File and Folder
• Directory
  • Parent Directory
  • Working Directory
• User
• Root or Root Directory
• Environments
• Backup
• Command, Command Line, Console
• Warning, Error, Permission Denied
• Segmentation Fault

Frequently Used Terms

• File and Folder
• Directory Path, Parent and Working Directory

Frequently Used Terms

User, Root and Home Directory

whoami

## emirtoker

Root directory symbol; “/”. Home directory symbol; “~”.

Frequently Used Terms

Environments and Backup

printenv  

Frequently Used Terms

Command Line, Command

Frequently Used Terms

Warning, Error, Permission Denied, Segmentation Fault

Directory Commands

• pwd (Print Working Directory)

• ls (List Directories)

• cd (Change Directory)

• mkdir (Make Directory)

Directory Commands - pwd

(Print Working Directory)

pwd

## /Users/emirtoker/Desktop/Dersler/Memurluk/Software_Tools_for_Earth_&_Environmental_Science/Software_Tools_R_Github/Presentation

Directory Commands - ls

(List Directories)

ls

## Presentation.Rproj
## Presentation_Week1_-_Data_and_Code.Rmd
## Presentation_Week1_-_Data_and_Code.html
## Presentation_Week2_-_Linux_and_Python.Rmd
## Presentation_Week2_-_Linux_and_Python.html
## Presentation_Week2_-_Linux_and_Python.pdf
## Presentation_Week3_-_Data_Sources_and_Download.Rmd
## Presentation_Week3_-_Data_Sources_and_Download.html
## Presentation_Week4_-_Introduction_to_R.Rmd
## Presentation_Week4_-_Introduction_to_R.html
## R_and_R_Studio.jpeg
## R_and_R_Studio.png
## R_logo.jpeg
## Richard.jpg
## The_Book_of_R.png
## The_Book_of_R_small.png
## VAPOR_HAIL_ANIME.gif
## Week1_rpubs.Rmd
## Week1_rpubs.html
## ai.png
## algorithm.png
## alma.jpg
## anaconda.png
## analysis.png
## apache_point.jpg
## arcgis.png
## ascii_1.png
## ascii_2.png
## aybe_seminar.png
## big_data1.png
## book_chp1.png
## book_flow.png
## cd1.png
## cd2.png
## cdo.png
## cdo1.png
## cdo2.png
## cdo3.png
## cdo4.png
## cdo5.png
## clear.png
## code.png
## command_line.png
## conda.png
## course_github.png
## coursera.png
## cp.png
## cp1.png
## cran_metu.png
## cran_turkey.png
## cru.png
## cygwin.png
## data_analytics.png
## data_assim.jpeg
## data_mining.svg
## data_types.png
## datacamp.png
## datacamp1.png
## datascience.png
## datashape.jpg
## datum.png
## deep.jpg
## download.png
## dropbox.png
## earthdata.png
## eda.png
## edx.png
## ensemble.png
## eobs.png
## era.png
## esgf.png
## exit.png
## extended_4th_week.png
## extended_syllabus.png
## extended_syllabus1.png
## extended_syllabus_3th_week.png
## filer_folder.png
## filezil.png
## filezilla.png
## find.png
## forecast.png
## generate.png
## gfs.png
## github.png
## gnu_logo.png
## gnu_logo_small.png
## grib.jpg
## grib_1.png
## grid_diff.jpg
## grid_sample.jpg
## gridded.jpg
## hdf5_structure.jpg
## help.png
## history.png
## iot.png
## jupyter.png
## jupyter_notebook.png
## kernel.jpg
## khanacademy.png
## knmi.png
## languages.png
## last_week.png
## last_week_2nd.png
## linus.jpeg
## linux_dist.png
## linux_logo.png
## machine.jpg
## mendeley.png
## metadata0.png
## metadata1.png
## meted.png
## mining.jpg
## mining1.jpg
## mkdir1.png
## mkdir2.png
## model.png
## mv.png
## my_profile
## mynewfile.png
## nc.png
## ncl.png
## ncl0.png
## ncl1.png
## ncl2.png
## ncll.png
## nco.png
## nco_diff.png
## ncview.png
## netcdf.png
## netcdf_1.png
## nwp_1.png
## nwp_2.png
## observation_data.png
## orcid.png
## os.png
## overleaf.png
## panoply.png
## printenv.png
## pwd_mac.png
## pwd_mac1.png
## pwd_win.png
## python.jpg
## python_term.png
## qgis.png
## r_book_week5.png
## r_classic1.png
## r_classic2.png
## r_clust.jpg
## r_comp.png
## r_corr.png
## r_dplyr.png
## r_inter.png
## r_linear.png
## r_screen1.png
## r_screen10.png
## r_screen11.png
## r_screen12.png
## r_screen13.png
## r_screen14.png
## r_screen15.png
## r_screen16.png
## r_screen17.png
## r_screen18.png
## r_screen19.png
## r_screen2.png
## r_screen20.png
## r_screen21.png
## r_screen22.png
## r_screen23.png
## r_screen24.png
## r_screen25.png
## r_screen3.png
## r_screen4.png
## r_screen5.png
## r_screen6.png
## r_screen7.png
## r_screen8.png
## r_screen9.png
## r_storms.gif
## r_terminal.png
## r_time.gif
## r_visual.png
## r_web.png
## raster_0.gif
## raster_dataset.png
## raster_vs_vector.png
## reanalysis.jpg
## researchgate.png
## rm.png
## robert_gentleman.jpg
## root.png
## root_fig.gif
## ross_lhaka.jpg
## rsconnect
## rstudio.png
## rstudio_cloud.png
## rstudio_down.png
## rstudio_logo.png
## rstudio_product.png
## rstudio_ubuntu.png
## shp.png
## shp_mask.png
## sil_notebook.Rmd
## sil_notebook.html
## sil_notebook.nb.html
## sil_notebook_files
## sil_rmarkdown.Rmd
## sil_rmarkdown.html
## sil_rmarkdown_files
## sil_sweave-concordance.tex
## sil_sweave.Rnw
## sil_sweave.log
## sil_sweave.tex
## simulation.jpg
## stackoverflow.png
## sublimetext.png
## syllabus.png
## syllabus_4th_week.png
## syllabus_5th.png
## teamviewer.png
## terminal.png
## terminal0.png
## terminal1.png
## th_1.gif
## th_1.png
## th_2.gif
## th_2.jpg
## th_3.gif
## touch.png
## udemy.png
## udemy1.png
## udemy_content_1.png
## udemy_hm1.png
## unix_develop.jpg
## unix_linux.png
## vector_type.png
## vector_type_1.jpg
## vector_vs_raster.png
## vi_0.png
## vi_1.png
## vi_2.png
## vi_3.png
## visual.jpg
## warning.png
## webminal.png
## week2_sil.Rmd
## week2_sil.html
## week2_sil.log
## week2_sil.tex
## week3.Rmd
## week3.html
## week4_extended_syllabus.png
## wetransfer.png
## wget.jpg
## what_data.svg
## win_folder.png
## wolfram-alpha.png
## wordclim.png
## zenodo-doi.png

Directory Commands - pwd and ls

Directory Commands - cd

(Change Directory)

cd Presentation/

Directory Commands - mkdir

(Make Directory)

mkdir <new_folder_name>

File Commands

• touch

• cat (Concatenate)

• rm (Remove)

• cp (Copy)

• mv (Move)

File Commands - touch

touch <my_new_file>

File Commands - cat

(Concatenate)

cat my_new_file

This is my new file. Hi!

File Commands - cp

(Copy)

cp my_new_file my_new_file2

File Commands - mv

(Move)

mv my_new_file2 my_new_file3

File Commands - rm

(Remove)

rm my_new_file my_new_file3

Special Commands

• find

• help

• history

• clear

• date and cal

• exit

Special Commands - find

find -name <name_of_file>

Special Commands - help

find --help

Special Commands - history

history

Special Commands - clear

clear

Special Commands - date and cal

date

## Fri Oct 11 16:01:26 +03 2019

cal

##     October 2019      
## Su Mo Tu We Th Fr Sa  
##        1  2  3  4  5  
##  6  7  8  9 10 _1_1 12  
## 13 14 15 16 17 18 19  
## 20 21 22 23 24 25 26  
## 27 28 29 30 31        
## 

Special Commands - exit

exit

vi Editor and Print Commands

• vi

• esc (default mode)

• i (insert mode)

• :q (just quit)

• :q! (don’t save and quit)

• :qw (write/save and quit)

• grep and echo

• head and tail

• sed (stream editor)

vi Editor and Print Commands - vi

vi Editor and Print Commands - esc

(Default Mode)

vi Editor and Print Commands - i

(Insert Mode)

vi Editor and Print Commands - :wq

(Write/Save and Quit)

vi Editor and Print Commands - grep and echo

grep my_profile

grep ITU my_profile

echo my_profile

name=Emir

echo $name

vi Editor and Print Commands - head and tail

head my_profile

tail my_profile

vi Editor and Print Commands - sed

(Stream Editor)

Replacing or substituting string;

sed 's/ITU/ODTU/' my_profile

sed '5d' my_profile 

Symbols

• | (and)
• > (assing)
• $ (special variable)
• ? (an unknown character)
• * (an unknown sroup of characters)

cat my_profile | sort

ls > my_list

x=3
echo $x

ls my*

ls ?y_list* 

Bash Script

touch my_bash_script.sh
vi my_bash_script.sh

x=5
y=3
echo $((x+y))

bash my_bash_script.sh

8

Practice

1. Learn where you are (Print your working directory)
2. Look at inside (list all documents and directories)
3. Create a new folder (make a directory,<my_new_dir>)
4. Go to the <my_new_dir> (change your directory)
5. Create a new file (touch it, file name : <my_new_file>)
6. Open this new file and write your name (vi-insert mode)
7. Save your work and close the file (write + quit)
8. Print your name on the screen (grep, tail, head, cat)
9. Put <my_new_file> at the parent directory (move it)
10. Go to parent directory (change directory with two dots)
11. Create a copy, name; <my_new_file_2>
12. Remove your first folder <my_new_dir>
13. List all documents and directories

Quiz

Introduction to Gnu/Linux

LINK

What is the Python

• Python is a programming language.
• Created by Guido van Rossum and first released in 1991.
• Python 2.0, released 2000, Python 3.0, released 2008.
• Python 2.7, the last release in the 2.x series, was extended to 2020.

Python in Terminal

webminal.org

GCC : GNU Compiler Collection

What is the Anaconda/Jupyter

Python in Anaconda/Jupyter

jupyter notebook